MolNFT v1 · #162381 · protein
Structure of imp-13 metallo-beta-lactamase in apo form (loop open)
6R79: “Structure of imp-13 metallo-beta-lactamase in apo form (loop open)”. X-ray diffraction, 4 ligands (GLY, ZN, NA), 7 pockets (best druggability 0.81). MolNFT v1 #162381 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6R79
- Type
- protein
- Length
- 874 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q7WYA8
- Ligands
- GLY, ZN, NA, PO4
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 220 | 28% helix, 30% strand | Q7WYA8 |
| B, D | Beta-lactamase (EC 3.5.2.6) | protein | 218 | 28% helix, 31% strand | Q7WYA8 |
| C | Beta-lactamase (EC 3.5.2.6) | protein | 218 | 28% helix, 30% strand | Q7WYA8 |
Ligands and binding sites
- GLY · Glycine · ligand · 13 copies · chains A, D, C
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains B
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
- BME · Beta-mercaptoethanol · additive · 6 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.81 | 0.83 | 79 | BME |
| 2 | 1020 | 0.78 | 0.80 | 77 | GLY |
| 3 | 410 | 0.67 | 0.80 | 42 | empty |
| 4 | 245 | 0.56 | 0.78 | 25 | empty |
| 5 | 88 | 0.43 | 0.79 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–C · 704 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 593 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 256 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6R79 · Structure of IMP-13 metallo-beta-lactamase in apo form (loop open) · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q7WYA8
- Elsewhere: RCSB PDB 6R79 · PDBe 6R79 · UniProt Q7WYA8
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